Porcupine is a protein belonging to the O-acyltransferase family, involved in catalyzing of palmitoylation of WNT proteins. WNT signalling has significant roles in many physiological functions, e.g.: hematopoiesis, homeostasis, neurogenesis, and apoptosis. Anomalous WNT signalling has been observed to be related to tumours generation, metabolic and neurodegenerative disorders. Therefore, compounds that inhibit this pathway are of great interest for the development of therapeutic approaches. For a better understanding of the common traits of such compounds, we have undertaken an in silico study in order to develop a valid ligand-based pharmacophore model based on a series of porcupine inhibitors. The best pharmacophore hypothesis found after the 3D QSAR validation process is represented by the following features: one hydrogen bond donor (D), three rings (R) and one hydrophobic centroid (H). The 3D-QSAR model obtained using the DRRRH hypothesis shows statistically significant parameters: correlation coefficients for the training set: R² of 0.90, and a predictive correlation coefficient for the test set, Q² of 0.86. The assessment of the pharmacophore model was also done by using the Enrichment calculator which provided very reliable metrics values (Receiver Operating Characteristic – ROC of 1; Robust Initial Enhancement – RIE of 17.97). Thereby, we obtained valuable results which can be further used in the virtual screening process for the discovery of new active compounds with potential anticancer activity.